30 lines
1.3 KiB
Org Mode
30 lines
1.3 KiB
Org Mode
* Biology Meets Programming: Bioinformatics for Beginners
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** Week 1
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*** DNA replication
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**** Origin of replication (ori)
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Locating an ori is key for gene therapy (e.g. viral vectors), to introduce a theraupetic gene.
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**** Exercises: computational approaches to find ori in Vibrio Cholerae
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***** Exercise: find Pattern
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We'll look for the *DnaA box* sequence, using a sliding window, in that case we will use the function [[./Code/Replication.py][Replication]] to find out how many times
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does a sequence appear in the genome.
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For the second part, we're going to calculate the frequency map of the sequences of length /k/, for that purpose we'll use [[./Code/FrequentWords.py][FrequentWords]]
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***** Exercise: Find the reverse complement of a sequence
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We're going to generate the reverse complement of a sequence, which is the complement of a sequence, read in the same direction (5' -> 3').
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In this case, we're going to use [[./Code/ReverseComplement.py][ReverseComplement]]
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After using our function on the Vibrio's Cholerae genome, we realize that some of the frequent k-mers are reverse complements of other frequent ones.
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*** Vocabulary
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- k-mer: subsquences of length /k/ in a biological sequence
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- Frequency map: sequence --> frequency of the sequence
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